With MassHunter the acquisition time stamp does not get updated until the end of the run, which is why you are seeing the incorrect time listed on data files that have not finished acquiring.

Agilent generally recommends that you wait until your method run has completed before loading it in a batch, but if you need to add the file to a batch before it has finished acquiring then your solution is the best fix (remove the file from the batch and re-add it).